A batch data pipeline that imports healthcare data from Synthea-generated FHIR JSON bundle files into XTDB, a temporal database with PostgreSQL wire protocol compatibility.

This project demonstrates how to:

• Parse and import FHIR R4 healthcare records efficiently
• Store clinical data in XTDB with temporal tracking
• Leverage XTDB's bitemporal capabilities for healthcare timeline queries

The importer extracts Patients, Encounters, and Conditions from FHIR bundles, mapping temporal fields to XTDB's _valid_from and _valid_to columns for point-in-time queries. All other resources found within each FHIR bundle are stored within the Patients table in its JSON format.

• Batch Import: Recursively processes all JSON files in a directory
• Bitemporal Support: Maps valid onset/abatement dates for Conditions to XTDB valid-time boundaries, as well as valid period_start/_end dates for Encounters.
• Connection Pooling: HikariCP for efficient database connections
• Structured Logging: SLF4J with Logback for operational visibility

• Java 21 or later
• Maven 3.9+
• XTDB running with PostgreSQL wire protocol enabled (Port: 5434)

cd xtdb-fhir
mvn clean package -DskipTests

This produces an executable JAR at target/xtdb-fhir-1.0-SNAPSHOT.jar.

java -jar target/xtdb-fhir-1.0-SNAPSHOT.jar <input-directory>

Example:

java -jar target/xtdb-fhir-1.0-SNAPSHOT.jar ./data/fhir

========================================
Import complete in  1250 ms
Files processed:    50
Patients:           50
Encounters:         152
Conditions:         287
All Other Resources:450
Errors:             0
========================================

Edit src/main/resources/application.properties:

db.host=localhost
db.port=5434
db.name=xtdb
db.user=xtdb
db.pool.size=5
db.pool.timeout=10000

xtdb-fhir/
├── src/
│   ├── main/
│   │   ├── java/com/example/
│   │   │   ├── Application.java           # CLI entry point
│   │   │   ├── config/
│   │   │   │   └── DatabaseConfig.java    # Connection & pooling logic
│   │   │   ├── service/
│   │   │   │   └── FHIRImportService.java # Core import logic
│   │   │   └── util/
│   │   │       └── JsonUtil.java          # JSON navigation utilities
│   │   └── resources/
│   │       ├── application.properties     # Database configuration
│   │       └── logback.xml                # Logging configuration
│   └── test/
│       └── java/com/example/              # Unit and integration tests
├── data/fhir/                             # Static Sample FHIR JSON files
└── pom.xml                                # Maven build configuration

FHIR JSON Files (Synthea)
        ↓
   JsonUtil.parseFile()
        ↓
┌───────────────────────────┐
│ Extract by resourceType:  │
│ • Patients                │
│ • Encounters              │
│ • Conditions              │
│ • Other (grouped by pt)   │
└───────────────────────────┘
        ↓
   Build XTDB Records
        ↓
   Insert via JDBC
        ↓
   XTDB Database

This enables queries like: "What conditions were active on March 15, 2020?"

# Unit tests (no database required)
mvn test

# Integration tests (requires running XTDB)
mvn verify

• Unit Tests: JSON parsing, configuration loading
• Integration Tests: Patient import, temporal queries, multi-resource bundles

The data/fhir/ directory contains 50+ synthetic patient records generated by Synthea. Each file is a FHIR Bundle containing:

• Patient demographics
• Encounter history
• Medical conditions
• Observations, medications, and other resources

MIT License - see LICENSE for details.